Some contigs are not scaffolded
rknx opened this issue · 0 comments
rknx commented
I have a plasmid that I am trying to stitch together. Based on molecular work and homology, I'm fairly certain two contigs (NODE_001 and NODE_051) below are part of same plasmid. However, in the final results, NODE_051 does not seem to be scaffolded with NODE_001.
Command
ragtag.py scaffold -C --debug -t 4 -d 250000 --aligner nucmer -o ragtag/qry ref.fa qry.fa
Please find relevant parts of debug outputs that may be of use:
ragtag.scaffold.debug.query.info.txt
NODE_001 CP018729.1 1.0 1.0 1.0
NODE_051 CP018729.1 1.0 1.0 1.0
NODE_130 CP018729.1 1.0 1.0 1.0
NODE_141 CP018729.1 1.0 1.0 1.0
NODE_165 CP018729.1 1.0 1.0 1.0
ragtag.scaffold.debug.unfiltered.paf
NODE_001 165349 16993 165349 + CP018729.1 211336 0 148354 148339 148356 0
NODE_001 165349 80 16993 + CP018729.1 211336 194424 211336 16912 16913 0
NODE_051 40607 37844 39333 - CP018729.1 211336 152188 153677 1446 1489 0
NODE_051 40607 72 32458 - CP018729.1 211336 162034 194428 32308 32395 0
NODE_130 5747 0 3339 + CP018729.1 211336 156050 159389 3339 3339 0
NODE_141 3861 0 3861 - CP018729.1 211336 148692 152553 3861 3861 0
NODE_165 524 0 524 - CP018729.1 211336 155185 155709 524 524 0
ragtag.scaffold.debug.filtered.paf
NODE_001 165349 16993 165349 + CP018729.1 211336 0 148354 148339 148356 0
NODE_001 165349 80 16993 + CP018729.1 211336 194424 211336 16912 16913 0
NODE_051 40607 37844 39333 - CP018729.1 211336 152188 153677 1446 1489 0
NODE_051 40607 72 32458 - CP018729.1 211336 162034 194428 32308 32395 0
NODE_130 5747 0 3339 + CP018729.1 211336 156050 159389 3339 3339 0
NODE_141 3861 0 3861 - CP018729.1 211336 148692 152553 3861 3861 0
NODE_165 524 0 524 - CP018729.1 211336 155185 155709 524 524 0
ragtag.scaffold.asm.paf
NODE_001 165349 16993 165349 + CP018729.1 211336 0 148354 148339 148356 0 NM:i:17 cg:Z:61867M1I59022M1I27465M
NODE_001 165349 80 16993 + CP018729.1 211336 194424 211336 16912 16913 0 NM:i:1 cg:Z:15091M1I1821M
NODE_051 40607 37844 39333 - CP018729.1 211336 152188 153677 1446 1489 0 NM:i:43 cg:Z:1489M
NODE_051 40607 72 32458 - CP018729.1 211336 162034 194428 32308 32395 0 NM:i:87 cg:Z:27321M2D1M3D16M1D87M3D3189M1I1771M
NODE_130 5747 0 3339 + CP018729.1 211336 156050 159389 3339 3339 0 NM:i:0 cg:Z:3339M
NODE_141 3861 0 3861 - CP018729.1 211336 148692 152553 3861 3861 0 NM:i:0 cg:Z:3861M
NODE_165 524 0 524 - CP018729.1 211336 155185 155709 524 524 0 NM:i:0 cg:Z:524M
But in the end, it appears that NODE_051 is not scaffolded together with NODE_001 in CP018729.1.
ragtag.scaffold.agp
CP018729.1_RagTag 1 165349 1 W NODE_001 1 165349 +
Chr0_RagTag 50040 90646 43 W NODE_051 1 40607 +
Chr0_RagTag 90647 90746 44 U 100 contig no na
rragtag.scaffold.stats
placed_sequences placed_bp unplaced_sequences unplaced_bp gap_bp gap_sequences
145 5285728 23 108456 16400 164
Why is NODE_051 not a part of the scaffold, and what parameters should I change to include it? Please let me know if you'd like the input files. Thanks.